In the manufacturing of integrated circuits, the sizes of integrated circuit devices are scaled down increasingly. For example, Complementary Metal-Oxide-Semiconductor (CMOS) Image Sensor (CIS) chips have increasingly smaller pixel sizes. Accordingly, the requirement in the DC and noise performance of the CIS chips becomes increasingly stricter. Conventional circuit formation processes thus cannot meet the strict requirements of the CIS chips. For example, Shallow Trench Isolation (STI) regions were used to isolate devices. In the formation of the STI regions, the silicon substrate, in which the STI regions are formed, suffers from damage caused by the formation of the STI regions. As a result, charges such as electrons are trapped at the interfaces between the STI regions and the silicon substrate. These charges cause background noise in the signals of the CIS chips.